The Anderson Lab

Here are resources our lab has produced for modeling species niches and distributions.

 

 

Papers:

 

Some Anderson lab papers on Maxent and niche modeling (see also Publications):

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• Kass et al. 2023 (a new version of wallace, a shiny app for niche modeling) PDF

• Galante et al. 2023 (changeRangeR, an R package for biodiversity change metrics) PDF

• Merow et al. 2022 (maskRangeR R package to post-process range maps) PDF

• Gavrutenko et al. 2021 (data-driven habitat masking to estimate current ranges) PDF

• Kass et al. 2021b (R package ENMeval 2.0, redesigned for metadata and expansion) PDF

• Kass et al. 2021a (support vector machines for postprocessing ranges of competitors) PDF

• Kass et al. 2020 (key plants improve models of a migrating species) PDF

• Soley et al. 2019 (repercussions of suitability level for phylogeography) PDF

• Bohl et al. 2019 (null-model approach for significance of ENMs) PDF

• Sanín and Anderson 2018 (an empirical BAM diagram – the first we know of!) PDF

• Galante et al. 2018 (species with few records, model selection/evaluation approaches) PDF

• Guevara et al. 2018 (biological realism and application of models to nonanalog conditions) PDF

• Kass et al. 2018 (new expandable platform for niche modeling with interactive GUI) PDF

• Anderson 2017 (including biotic interactions in niche/distribution) PDF

• Boria et al. 2017 (variability among co-optimal models and implications for cross-time uses) PDF

• Phillips et al. 2017 (open-source release of Maxent!) PDF

• Soley-Guardia et al. 2016 (removing marginal localities to avoid niche overestimation) PDF

• Aiello-Lammens et al. 2015 (R package for spatial thinning of occurrence localities) PDF

• Anderson 2015 (not peer-reviewed): intro to niche modeling in Spanish, English, and French PDF

• Boria et al. 2014 (sampling bias, overfitting, and spatial filtering of occurrence localities) PDF

• Gutiérrez et al. 2014 (biotic interactions and effects on population connectivity) PDF​

• Muscarella et al. 2014 (R package ENMeval, for selecting optimal model settings) PDF

• Radosavljevic and Anderson 2014 (model complexity, evaluation, and overfitting) PDF

• Soley-Guardia et al. 2014 (spatially and environmentally marginal localities) PDF​

• Varela et al. 2014. (sampling bias and a simulated species) PDF

• Anderson 2013 (using niche models to predict across space or time) PDF

• Shcheglovitova and Anderson 2013 (tuning model settings for species with few records) PDF

• Anderson 2012 (use of museum/herbarium data for niche modeling) PDF

• Anderson and Gonzalez 2011 (spatially biased sampling; program settings/model complexity) PDF

• Anderson and Raza 2010 (principles for study-region selection) PDF

• Phillips et al. 2006 (documentation of Maxent/worked examples) PDF

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Books:

 

A book on niches, distributions, and niche modeling (see also Publications):

 

• Peterson et al. 2011 Princeton University Press

 

 

 

 

 

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Software:

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GUI apps:

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Wallace:

Kass, J. M., B. Vilela, M. E. Aiello-Lammens, R. Muscarella, C. Merow, and R. P. Anderson. WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. Methods in Ecology and Evolution. 9:1151-1156. PDF

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Kass, J. M., G. E. Pinilla-Buitrago, A. Paz, B. A. Johnson, V. Grisales-Betancur, S. I. Meenan, D. Attali, O. Broennimann, P. J. Galante, B. S. Maitner, H. L. Owens, S. Varela, C. Merow, M. E. Aiello-Lammens, M. E. Blair, and R. P. Anderson. 2023. wallace v2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions. Ecography, e06547. PDF.

 

Package documentation here​.

Visit the Wallace website.

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Maxent:

Phillips, S. J., R. P. Anderson, and R. E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190:231-259. PDF

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Phillips, S. J., R. P. Anderson, M. Dudík, R. E. Schapire, M. E. Blair. 2017. Opening the black box: an open–source release of Maxent. Ecography. 40:887-893. PDF

 

Visit the new Maxent web page at AMNH Center for Biodiversity and Conservation. 

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R Packages:

   

ENMeval:

Kass, J. M., Muscarella, R., Galante, P. J., Bohl, C. L., Pinilla-Buitrago, G. E., Boria, R. A., Soley-Guardia, M., and Anderson, R. P. 2021. ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions. Methods in Ecology and Evolution (12) 9:1602-1608. PDF. CRAN documentation here.

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Muscarella, R., P. J. Galante, M. Soley-Guardia, R. A. Boria, J. M. Kass, M. Uriarte, and R. P. Anderson. 2014. ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for MAXENT ecological niche models. Methods in Ecology and Evolution. 5:1198-1205 PDF. 

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spThin:

Aiello-Lammens, M. E., R. A. Boria, A. Radosavljevic, B. Vilela, and R. P. Anderson. 2015. spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography. 38:541-545. PDF

CRAN documentation found here.

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Podcasts/Videos/Slides:

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Podcasts:

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Head over to the Wallace YouTube channel to learn more about ecological niche modeling and the developers of Wallace!  The team is working to expand the content on the channel and plans to release more videos.  We are planning on creating more software tutorials, discussions about current research in the field, applications of models made using Wallace, interviews with the team of researchers behind the software, and much more. Visit YouTube 

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(The following podcast was produced as part of the 2017 Blavatnik Science Symposium, held at the New York Academy of Sciences in New York.  It features William Anderegg, Nicolás Young, and Robert Anderson.)

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New York Academy of Sciences. 2017. Rethinking Climate Change [podcast]. Listen here.

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Webinars on niche modeling:

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(The following webinar was part of the "Modelado de Distribuciones Potenciales" series, organized by Angela Cuervo.)

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Anderson, R. P. 21 May 2018. "El software Wallace para modelar nichos y distribuciones: Un coche con motor R, volante de ratón y cerebro de humano." Broadcast from the City College of New York, City University of New York. Watch on YouTube.

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(The following webinar was the "37th Global Online Biodiversity Informatics Seminar" in the Biodiversity Informatics Training Curriculum organized by Town Peterson.)

 

Kass, J. M. 9 May 2018. "WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion." Broadcast from the City College of New York, City University of New York. Watch on YouTube.

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(The following webinar was the "6th Global Online Biodiversity Informatics Seminar" in the Biodiversity Informatics Training Curriculum organized by Town Peterson.)

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Anderson, R. P. 28 August 2014. "Methods matter: estimates of suitability and population connectivity in tropical mammals using ecological niche modeling." Broadcast from the City College of New York, City University of New York. Watch on YouTube or the group's Google+ page.

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Video presentations on various topics within a niche modeling framework:

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(The following presentation was given at the 2017 Blavatnik Science Symposium, held at the New York Academy of Sciences in New York.)

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Anderson, R. "Modeling shifts in the geographic distributions of animals in response to climate change". 2017 Blavatnik Science Symposium, New York Academy of Sciences, New York, New York. 17–18 July 2017. View here.

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(The following presentation was given at the Human Health in the Face of Climate Change Conference in Barcelona, Spain.)

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Anderson, R.P. "Crossing Scales in Biodiversity Prediction for Human Health Applications". Human Health in the Face of Climate Change: Science, Medicine, and Adaptation, Barcelona, Spain, 14-15 May 2015. View here.

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(The following four presentations are part of the Ecological Niche Modeling section of Biodiversity Informatics Training Curriculum organized by Town Peterson.  They derive from the course "Calibrating Ecological Niche Models: integrating climate change mediated distributional shifts and phylogenetic frameworks in biodiversity conservation," Universidade dos Açores, Ponta Delgada, Portugal, 27–30 January 2014.)

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Anderson, R. P., Yesson, C. 27-30 January 2014. "Models in General".  Watch on YouTube.

Anderson, R. P., Yesson, C. 27-30 January 2014. "Model Complexity".  Watch on YouTube.

Anderson, R. P., Yesson, C. 27-30 January 2014. "Niches to Distributions".  Watch on YouTube.

Anderson, R. P., Yesson, C. 27-30 January 2014. "Model Transfer".  Watch on YouTube.

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Slides from presentations on niche modeling theory and practice:

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(These were developed for various training courses/workshops on niche-based modeling of species distributions, culminating in the course "Modelos de nicho y distribuciones de especies," Instituto Venezolano de Investigaciones Científicas, near Caracas, Venezuela 14–18 May 2012.)

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• Anderson, R. P. Evaluations and complexity PDF

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• Anderson, R. P. Transfers and climate change PDF

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• Anderson, R. P. Niche theory PDF

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• Anderson, R. P. Maxent overview PDF

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